I was looking this up when I first saw the Prometheus trailer and apparently, according to Scott, Prometheus takes place before Alien, but isn't tied with the franchise
"A script by Spaihts acted as a prequel to the events of the Alien films, but Scott opted for a different direction to avoid repeating cues from those films. In late 2010, he brought Lindelof onto the project to rewrite Spaihts' script, and together they developed a separate story that precedes the story of Alien but is not directly connected to that franchise. According to Scott, though the film shares "strands of Alien's DNA, so to speak", and takes place in the same universe, Prometheus will explore its own mythology and ideas."